1 Gene Level copy number file from TCGA

Downloading the Gene level Copy number files from TCGA, I computed CIN in the following way: - gene CNV > 2.25 = Amp - gene CNV < 1.75 = Del

I have mapped cytobands to gene entrez ids using org.Hs.egMAP and using the cytobands I extract the gene level CIN which will be added at cytoband level for all the genes in that cytoband across all the different cases that we have from TCGA-SARC

Plots: 1- Overall boxplots: for each chromosome all the cytoband CIN per sarcoma type

1b - Overall heatmap: for each chromosome a heatmap with all the CIN per cytobands and annotation on the side for each sarcoma type

2- HRD boxplots: The same as before but separating HRDhigh/low

2b - is there any cytoband differentially expressed between HRD/low groups in particular?
3- Make enrichment in those cytobands :)

1.1 Chromosome 1 Cytobands

1.2 Chromosome 2 Cytobands

1.3 Chromosome 3 Cytobands

1.4 Chromosome 4 Cytobands

1.5 Chromosome 5 Cytobands

1.6 Chromosome 6 Cytobands

1.7 Chromosome 7 Cytobands

1.8 Chromosome 8 Cytobands

1.9 Chromosome 9 Cytobands

1.10 Chromosome 10 Cytobands

1.11 Chromosome 11 Cytobands

1.12 Chromosome 12 Cytobands

1.13 Chromosome 13 Cytobands

1.14 Chromosome 14 Cytobands

1.15 Chromosome 15 Cytobands

1.16 Chromosome 16 Cytobands

1.17 Chromosome 17 Cytobands

1.18 Chromosome 18 Cytobands

1.19 Chromosome 19 Cytobands

1.20 Chromosome 20 Cytobands

1.21 Chromosome 21 Cytobands

1.22 Chromosome 22 Cytobands

1.23 ——————- ChromoMAP ———————–

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## ** __**|__ * __* __ * __ __ * __ *|  |  |* __ * __ **
## **|__**|  |*|  *|__|*|  |  |*|__|*|  |  |*|_ |*|__|**
## ***********************************************|   **
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## OUTPUT: 
## Number of Chromosome sets: 1 
## Number of Chromosomes in set  1 : 2 
## Processing data.. 
## Number of annotations in data set  1 : 9547 
## Visualizing..
## ********************************** __ __ ************
## ** __**|__ * __* __ * __ __ * __ *|  |  |* __ * __ **
## **|__**|  |*|  *|__|*|  |  |*|__|*|  |  |*|_ |*|__|**
## ***********************************************|   **
## *****************************************************
## OUTPUT: 
## Number of Chromosome sets: 1 
## Number of Chromosomes in set  1 : 2 
## Processing data.. 
## Number of annotations in data set  1 : 9547 
## Visualizing..

Copyright © 2022 Alicia Pliego. FTP lab. All rights reserved.